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2n2f

Solution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Receptor

Method: SOLUTION NMR Dmax: 21.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dynorphin A(1-13)

OrganismNot specified

UniProt P01213

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 207–219 Fragment：residues 207-219 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.1；280 K；Pressure ambient NMR sample composition：1 mM [U-15N-GFLI] Dynorphin 1, 150 mM potassium chloride, 40 mM [U-2H] MES, 100 uM DSS, 10 uM KOR, 8 mM DDM, 1.6 mM CHS, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-15N-GFLIR; U-13C-R] Dynorphin 1, 150 mM potassium chloride, 40 mM [U-2H] MES, 100 uM DSS, 10 uM KOR, 8 mM DDM, 1.6 mM CHS, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2N2F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8F7W Gi bound kappa-opioid receptor in complex with dynorphin Deposited 2022-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain P 207–214（8 aa） Fragment：UNP residues 207-214
Not recorded CLR CHOLESTEROL × 3 PLM PALMITIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å
8VJU Structure of Human Neurolysin in complex with dynorphin A13 peptide Deposited 2024-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 207–219（13 aa）
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 1.99 Å R-free 0.218
8VJV Structure of Human Neurolysin in complex with dynorphin A8(1-8) peptide Deposited 2024-01-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 207–214（8 aa）
Not recorded ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.12 Å R-free 0.249
9CCE structure of DYNA_1b7 Deposited 2024-06-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 207–223（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.1 M Phosphate/citrate pH 4.2 and 40 % v/v PEG 300
Resolution 3.15 Å R-free 0.313
9CCE structure of DYNA_1b7 Deposited 2024-06-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 207–223（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.1 M Phosphate/citrate pH 4.2 and 40 % v/v PEG 300
Resolution 3.15 Å R-free 0.313
9CCF Crystal Structure of DA7-2 Deposited 2024-06-21 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 207–223（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M Sodium acetate pH 4.6 and 25% (v/v) PEG 550 MME
Resolution 4.00 Å R-free 0.296
9CCF Crystal Structure of DA7-2 Deposited 2024-06-21 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 207–223（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M Sodium acetate pH 4.6 and 25% (v/v) PEG 550 MME
Resolution 4.00 Å R-free 0.296
9L60 Gi-bound kappa opioid receptor in complex with dynorphin and positive allosteric modulator MPAM-15 Deposited 2024-12-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain P 207–219（13 aa）
Not recorded CLR CHOLESTEROL × 2 A1D6C 9-[5-(3-chlorophenyl)furan-2-yl]-3,3,6,6-tetramethyl-4,5,7,9-tetrahydro-2~{H}-xanthene-1,8-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PDYN_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–13； UniProt 207–219

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2n2f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2n2f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2n2f
Deposition date deposition_date2015-05-06
Structure title titleSolution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Receptor
Keywords keywordsGPCR, HORMONE RECEPTOR; HORMONE RECEPTOR
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier7.81 Å
Radius of gyration Rg (electron density) rg_electron7.86 Å
Forward intensity I(0) i03488710.00
Molecular weight molecular_weight16090.0 kDa
Excluded volume excluded_volume21029 ų
Envelope volume envelope_volume6872 ų
Hydration-shell volume shell_volume6436 ų
Envelope diameter envelope_diameter33.9 Å
Shell Rg shell_rg14.64 Å
Envelope Rg envelope_rg10.01 Å
Shape Rg shape_rg7.83 Å
Total Rg total_rg8.96 Å
Total atoms total_atoms2450
Residues n_residues130
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax21.5 Å
Rg (real space) rg_real7.53 Å
Rg uncertainty (real space) rg_real_error0.03 Å
I(0) (real space) i0_real3.3680e+06
I(0) uncertainty (real space) i0_real_error2.0670e+04
Rg (reciprocal space) rg_reciprocal7.90 Å
I(0) (reciprocal space) i0_reciprocal3489000.0000
Solution quality estimate total_estimate0.6817
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary8.4 Å
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.552
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha7.8070
Highest regularization parameter α highest_alpha2652.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 1.000; Stabil: 0.967; Sysdev: 0.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)